Having the tops of the pots covered be it perlite,clay, gravel etc is a great way to have thousands of little hair line roots at the crown of the plant covering the top layer of the coco. So yes worth doing and it will have no ill effects at all.
Get some magnecal especially when growing in coco. Also for your feed mixes use the custom nutrient guide on the canna site. Home | CANNA Gardening CANADA
I always use the light feed option, if I use normal or heavy feed I get white tips on the leaves and this lets me know to back of the nutes...